diff genomad_end_to_end.xml @ 1:edb671f0661e draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ commit dddf8b42771f66318f3325607bbd7aa33a3716b5

--- a/genomad_end_to_end.xml	Tue Jun 18 14:28:44 2024 +0000
+++ b/genomad_end_to_end.xml	Mon Oct 07 11:51:02 2024 +0000
@@ -2,7 +2,7 @@
     <description>identify virus and plasmid genomes from nucleotide sequences</description>
     <macros>
         <token name="@TOOL_VERSION@">1.8.0</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@MIN_DB_VERSION@">1.2</token>  <!-- https://portal.nersc.gov/genomad/__data__/releases.txt -->
         <xml name="summary_output_macro" tokens="type">
             <data name="summary_@TYPE@_fna" format="fasta" from_work_dir="output/sequence_summary/sequence_@TYPE@.fna" label="${tool.name} on ${on_string}: @TYPE@ fasta"/>
@@ -59,6 +59,9 @@
             '$DATABASE.fields.path'
     ]]></command>
     <inputs>
+        <param name="license" type="boolean" checked="false" label="Agree with geNomad license?" help="geNomad is free to use for internal use, research &amp; development, non-commercial use, purposes only.">
+            <validator type="expression" message="You need to agree to the geNomad license in order to use this tool. License is linked in the help below.">value</validator>
+        </param>
         <param argument="INPUT" type="data" format="fasta" label="Input sequences" help="geNomad will work for isolate genomes, metagenomes, and metatranscriptomes"/>
         <param name="DATABASE" type="select" label="Reference data" help="">
             <options from_data_table="genomad"/>
@@ -114,6 +117,7 @@
     </outputs>
     <tests>
         <test>
+            <param name="license" value="true"/>
             <param name="INPUT" value="GCF_009025895.1_ASM902589v1_genomic.fna" ftype="fasta"/>
             <param name="DATABASE" value="1.2"/>
             <section name="annotation">
@@ -172,6 +176,8 @@
 
 This Galaxy tool executed the ent-to-end geNomad workflow.
 
+geNomad is free to use for internal use, research &amp; development, non-commercial use, purposes **only**. Check out the full `License`_.
+
 Usage
 .....
 
@@ -230,6 +236,8 @@
 
 plasmid/virus genes/proteins: gives the nucleotide and aminoaced sequences of the annotated genes
 
+.. _License: https://raw.githubusercontent.com/apcamargo/genomad/refs/heads/main/LICENSE
+
     ]]></help>
     <citations>
         <citation type="doi">10.1038/s41587-023-01953-y</citation>